Starting phenix.real_space_refine on Wed Sep 17 06:47:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lsk_63358/09_2025/9lsk_63358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lsk_63358/09_2025/9lsk_63358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lsk_63358/09_2025/9lsk_63358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lsk_63358/09_2025/9lsk_63358.map" model { file = "/net/cci-nas-00/data/ceres_data/9lsk_63358/09_2025/9lsk_63358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lsk_63358/09_2025/9lsk_63358.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4256 2.51 5 N 1024 2.21 5 O 1102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6422 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3189 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 416} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3189 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 416} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'CIT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'CIT': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.80, per 1000 atoms: 0.28 Number of scatterers: 6422 At special positions: 0 Unit cell: (68.4584, 74.232, 107.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1102 8.00 N 1024 7.00 C 4256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 349.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 2 sheets defined 81.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'A' and resid 50 through 72 removed outlier: 3.829A pdb=" N ILE A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 4.489A pdb=" N VAL A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 167 removed outlier: 3.836A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 204 through 237 removed outlier: 4.257A pdb=" N TYR A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 288 removed outlier: 3.525A pdb=" N THR A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 3.612A pdb=" N GLY A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 Processing helix chain 'A' and resid 336 through 348 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 359 through 385 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 419 through 446 Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 50 through 72 removed outlier: 3.867A pdb=" N ILE B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 81 through 96 Processing helix chain 'B' and resid 100 through 112 Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.660A pdb=" N LEU B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 167 removed outlier: 4.278A pdb=" N LEU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 169 through 177 Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 204 through 237 removed outlier: 3.998A pdb=" N TYR B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.795A pdb=" N SER B 241 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 237 through 242' Processing helix chain 'B' and resid 264 through 288 Processing helix chain 'B' and resid 299 through 315 removed outlier: 3.536A pdb=" N GLY B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 336 Processing helix chain 'B' and resid 336 through 348 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 359 through 385 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'B' and resid 419 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 23 518 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1973 1.34 - 1.46: 1044 1.46 - 1.58: 3458 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 6545 Sorted by residual: bond pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.48e+00 bond pdb=" N GLY A 403 " pdb=" CA GLY A 403 " ideal model delta sigma weight residual 1.447 1.475 -0.028 1.09e-02 8.42e+03 6.64e+00 bond pdb=" N ASP A 407 " pdb=" CA ASP A 407 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.50e+00 bond pdb=" N SER A 412 " pdb=" CA SER A 412 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.30e+00 bond pdb=" N ASN A 401 " pdb=" CA ASN A 401 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.34e-02 5.57e+03 5.20e+00 ... (remaining 6540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 8728 2.19 - 4.38: 125 4.38 - 6.56: 23 6.56 - 8.75: 4 8.75 - 10.94: 3 Bond angle restraints: 8883 Sorted by residual: angle pdb=" N MET A 399 " pdb=" CA MET A 399 " pdb=" C MET A 399 " ideal model delta sigma weight residual 113.55 105.02 8.53 1.26e+00 6.30e-01 4.58e+01 angle pdb=" CA GLY A 403 " pdb=" C GLY A 403 " pdb=" O GLY A 403 " ideal model delta sigma weight residual 122.29 117.45 4.84 8.10e-01 1.52e+00 3.57e+01 angle pdb=" CA ASP A 407 " pdb=" CB ASP A 407 " pdb=" CG ASP A 407 " ideal model delta sigma weight residual 112.60 117.91 -5.31 1.00e+00 1.00e+00 2.82e+01 angle pdb=" C ASP A 407 " pdb=" CA ASP A 407 " pdb=" CB ASP A 407 " ideal model delta sigma weight residual 110.85 119.66 -8.81 1.70e+00 3.46e-01 2.69e+01 angle pdb=" N ASP A 407 " pdb=" CA ASP A 407 " pdb=" C ASP A 407 " ideal model delta sigma weight residual 111.36 105.79 5.57 1.09e+00 8.42e-01 2.62e+01 ... (remaining 8878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3519 17.43 - 34.87: 240 34.87 - 52.30: 31 52.30 - 69.73: 6 69.73 - 87.17: 2 Dihedral angle restraints: 3798 sinusoidal: 1386 harmonic: 2412 Sorted by residual: dihedral pdb=" CA GLY A 396 " pdb=" C GLY A 396 " pdb=" N LEU A 397 " pdb=" CA LEU A 397 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" C ASP A 407 " pdb=" N ASP A 407 " pdb=" CA ASP A 407 " pdb=" CB ASP A 407 " ideal model delta harmonic sigma weight residual -122.60 -133.42 10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA ARG B 402 " pdb=" C ARG B 402 " pdb=" N GLY B 403 " pdb=" CA GLY B 403 " ideal model delta harmonic sigma weight residual 180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 3795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 865 0.056 - 0.111: 193 0.111 - 0.167: 18 0.167 - 0.222: 2 0.222 - 0.278: 2 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA ASP A 407 " pdb=" N ASP A 407 " pdb=" C ASP A 407 " pdb=" CB ASP A 407 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU A 408 " pdb=" N LEU A 408 " pdb=" C LEU A 408 " pdb=" CB LEU A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA MET A 399 " pdb=" N MET A 399 " pdb=" C MET A 399 " pdb=" CB MET A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.27e-01 ... (remaining 1077 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 332 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C PHE B 332 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE B 332 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 333 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 65 " -0.012 2.00e-02 2.50e+03 1.00e-02 1.77e+00 pdb=" CG PHE B 65 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 65 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 65 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 65 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 332 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C PHE A 332 " 0.022 2.00e-02 2.50e+03 pdb=" O PHE A 332 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 333 " -0.007 2.00e-02 2.50e+03 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 346 2.73 - 3.27: 7044 3.27 - 3.81: 11277 3.81 - 4.36: 12500 4.36 - 4.90: 22369 Nonbonded interactions: 53536 Sorted by model distance: nonbonded pdb=" O GLY A 127 " pdb=" OG SER A 131 " model vdw 2.185 3.040 nonbonded pdb=" O TYR A 144 " pdb=" OG1 THR A 147 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR B 264 " pdb=" OE1 GLU B 267 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 204 " pdb=" OE1 GLU A 206 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASP B 171 " pdb=" N ARG B 172 " model vdw 2.239 3.120 ... (remaining 53531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 258 or (resid 259 and (name N or name CA or nam \ e C or name O or name CB )) or resid 260 through 501)) selection = (chain 'B' and (resid 18 through 248 or (resid 249 through 259 and (name N or na \ me CA or name C or name O or name CB )) or resid 260 through 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6545 Z= 0.209 Angle : 0.681 10.939 8883 Z= 0.408 Chirality : 0.045 0.278 1080 Planarity : 0.003 0.024 1085 Dihedral : 11.950 87.168 2270 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.39 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.30), residues: 854 helix: 1.78 (0.20), residues: 672 sheet: None (None), residues: 0 loop : -2.01 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 428 TYR 0.016 0.001 TYR A 300 PHE 0.023 0.002 PHE B 65 TRP 0.010 0.001 TRP A 303 HIS 0.003 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6545) covalent geometry : angle 0.68077 ( 8883) hydrogen bonds : bond 0.06246 ( 518) hydrogen bonds : angle 4.64799 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.247 Fit side-chains REVERT: B 231 ASP cc_start: 0.9021 (t70) cc_final: 0.8368 (t0) REVERT: B 350 ASP cc_start: 0.7845 (t0) cc_final: 0.7643 (t0) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.4805 time to fit residues: 50.8292 Evaluate side-chains 68 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN B 352 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.063060 restraints weight = 12688.840| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.95 r_work: 0.2700 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6545 Z= 0.151 Angle : 0.579 12.318 8883 Z= 0.299 Chirality : 0.041 0.139 1080 Planarity : 0.004 0.030 1085 Dihedral : 5.916 51.621 934 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.07 % Allowed : 11.16 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.29), residues: 854 helix: 2.07 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 172 TYR 0.019 0.001 TYR A 31 PHE 0.020 0.001 PHE B 87 TRP 0.018 0.001 TRP A 239 HIS 0.003 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6545) covalent geometry : angle 0.57860 ( 8883) hydrogen bonds : bond 0.04631 ( 518) hydrogen bonds : angle 4.35420 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.275 Fit side-chains REVERT: A 131 SER cc_start: 0.8732 (m) cc_final: 0.8440 (m) REVERT: A 389 ILE cc_start: 0.9096 (mt) cc_final: 0.8883 (mp) REVERT: B 103 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8686 (mt-10) REVERT: B 231 ASP cc_start: 0.8972 (t70) cc_final: 0.8440 (t0) REVERT: B 304 MET cc_start: 0.8819 (ttt) cc_final: 0.8480 (ttm) REVERT: B 350 ASP cc_start: 0.8241 (t0) cc_final: 0.7702 (t0) outliers start: 7 outliers final: 2 residues processed: 76 average time/residue: 0.4949 time to fit residues: 39.9969 Evaluate side-chains 70 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 170 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 0.0980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN B 352 GLN ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.085629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.063088 restraints weight = 12811.046| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.90 r_work: 0.2744 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6545 Z= 0.128 Angle : 0.549 11.207 8883 Z= 0.282 Chirality : 0.040 0.131 1080 Planarity : 0.003 0.034 1085 Dihedral : 5.715 48.287 932 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.92 % Allowed : 13.46 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.30), residues: 854 helix: 2.24 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -2.15 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 172 TYR 0.017 0.001 TYR A 31 PHE 0.017 0.001 PHE B 65 TRP 0.014 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6545) covalent geometry : angle 0.54938 ( 8883) hydrogen bonds : bond 0.04444 ( 518) hydrogen bonds : angle 4.21457 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.391 Fit side-chains REVERT: A 131 SER cc_start: 0.8779 (m) cc_final: 0.8479 (m) REVERT: B 50 ASP cc_start: 0.8195 (p0) cc_final: 0.7981 (p0) REVERT: B 103 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8615 (mt-10) REVERT: B 231 ASP cc_start: 0.8982 (t70) cc_final: 0.8381 (t70) REVERT: B 304 MET cc_start: 0.8737 (ttt) cc_final: 0.8386 (ttm) outliers start: 6 outliers final: 2 residues processed: 76 average time/residue: 0.4857 time to fit residues: 39.4408 Evaluate side-chains 70 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 170 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN ** B 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.087006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.064322 restraints weight = 12987.637| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.94 r_work: 0.2756 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6545 Z= 0.121 Angle : 0.536 11.724 8883 Z= 0.275 Chirality : 0.040 0.133 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.539 44.695 932 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.29 % Allowed : 14.83 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.30), residues: 854 helix: 2.31 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.15 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.017 0.001 TYR B 31 PHE 0.016 0.001 PHE B 65 TRP 0.012 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6545) covalent geometry : angle 0.53551 ( 8883) hydrogen bonds : bond 0.04295 ( 518) hydrogen bonds : angle 4.13892 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.281 Fit side-chains REVERT: B 50 ASP cc_start: 0.8224 (p0) cc_final: 0.7986 (p0) REVERT: B 103 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: B 141 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 231 ASP cc_start: 0.9000 (t70) cc_final: 0.8375 (t70) REVERT: B 304 MET cc_start: 0.8764 (ttt) cc_final: 0.8408 (ttm) REVERT: B 350 ASP cc_start: 0.8395 (t0) cc_final: 0.7897 (t0) outliers start: 15 outliers final: 5 residues processed: 80 average time/residue: 0.4784 time to fit residues: 40.8061 Evaluate side-chains 78 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.064188 restraints weight = 13179.973| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.96 r_work: 0.2752 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6545 Z= 0.127 Angle : 0.537 11.070 8883 Z= 0.275 Chirality : 0.039 0.132 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.432 43.600 932 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.45 % Allowed : 15.14 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.30), residues: 854 helix: 2.32 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.09 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.016 0.001 TYR A 31 PHE 0.015 0.001 PHE B 65 TRP 0.012 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6545) covalent geometry : angle 0.53659 ( 8883) hydrogen bonds : bond 0.04285 ( 518) hydrogen bonds : angle 4.13282 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: B 50 ASP cc_start: 0.8236 (p0) cc_final: 0.8023 (p0) REVERT: B 103 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8652 (mt-10) REVERT: B 231 ASP cc_start: 0.9006 (t70) cc_final: 0.8364 (t70) REVERT: B 304 MET cc_start: 0.8758 (ttt) cc_final: 0.8402 (ttm) REVERT: B 350 ASP cc_start: 0.8411 (t0) cc_final: 0.7881 (t0) outliers start: 16 outliers final: 9 residues processed: 82 average time/residue: 0.4468 time to fit residues: 39.2234 Evaluate side-chains 81 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.063980 restraints weight = 13071.732| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.96 r_work: 0.2757 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6545 Z= 0.120 Angle : 0.531 11.365 8883 Z= 0.271 Chirality : 0.040 0.137 1080 Planarity : 0.003 0.036 1085 Dihedral : 5.327 43.027 932 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.06 % Allowed : 15.44 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.30), residues: 854 helix: 2.37 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.11 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.016 0.001 TYR B 31 PHE 0.015 0.001 PHE B 65 TRP 0.008 0.001 TRP A 239 HIS 0.002 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6545) covalent geometry : angle 0.53130 ( 8883) hydrogen bonds : bond 0.04185 ( 518) hydrogen bonds : angle 4.09467 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 417 MET cc_start: 0.8841 (tpt) cc_final: 0.8485 (mmm) REVERT: B 50 ASP cc_start: 0.8150 (p0) cc_final: 0.7936 (p0) REVERT: B 103 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8597 (mt-10) REVERT: B 141 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8446 (mp) REVERT: B 231 ASP cc_start: 0.9001 (t70) cc_final: 0.8361 (t0) REVERT: B 304 MET cc_start: 0.8742 (ttt) cc_final: 0.8383 (ttm) REVERT: B 350 ASP cc_start: 0.8416 (t0) cc_final: 0.7904 (t0) outliers start: 20 outliers final: 11 residues processed: 86 average time/residue: 0.4486 time to fit residues: 41.2430 Evaluate side-chains 84 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 0.0010 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.087316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.064284 restraints weight = 12933.917| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.95 r_work: 0.2776 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6545 Z= 0.126 Angle : 0.544 11.112 8883 Z= 0.279 Chirality : 0.040 0.130 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.257 43.403 932 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.91 % Allowed : 15.90 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.30), residues: 854 helix: 2.21 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -1.91 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.016 0.001 TYR A 31 PHE 0.015 0.001 PHE B 65 TRP 0.010 0.001 TRP A 239 HIS 0.001 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6545) covalent geometry : angle 0.54367 ( 8883) hydrogen bonds : bond 0.04233 ( 518) hydrogen bonds : angle 4.13233 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 417 MET cc_start: 0.8958 (tpt) cc_final: 0.8585 (mmm) REVERT: B 50 ASP cc_start: 0.8250 (p0) cc_final: 0.8043 (p0) REVERT: B 103 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8657 (mt-10) REVERT: B 141 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8480 (mp) REVERT: B 178 VAL cc_start: 0.9030 (t) cc_final: 0.8821 (p) REVERT: B 231 ASP cc_start: 0.9047 (t70) cc_final: 0.8400 (t0) REVERT: B 304 MET cc_start: 0.8828 (ttt) cc_final: 0.8478 (ttm) REVERT: B 350 ASP cc_start: 0.8448 (t0) cc_final: 0.7948 (t0) outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.4307 time to fit residues: 38.3366 Evaluate side-chains 85 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.087125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.064355 restraints weight = 12982.595| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.95 r_work: 0.2759 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6545 Z= 0.132 Angle : 0.534 11.154 8883 Z= 0.274 Chirality : 0.039 0.129 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.174 44.493 932 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.06 % Allowed : 15.90 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.30), residues: 854 helix: 2.37 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.96 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.017 0.001 TYR A 31 PHE 0.015 0.001 PHE B 65 TRP 0.034 0.001 TRP A 239 HIS 0.001 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 6545) covalent geometry : angle 0.53428 ( 8883) hydrogen bonds : bond 0.04291 ( 518) hydrogen bonds : angle 4.11774 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.193 Fit side-chains REVERT: A 350 ASP cc_start: 0.8036 (p0) cc_final: 0.7673 (p0) REVERT: A 417 MET cc_start: 0.8930 (tpt) cc_final: 0.8555 (mmm) REVERT: B 50 ASP cc_start: 0.8225 (p0) cc_final: 0.8013 (p0) REVERT: B 103 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: B 141 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8471 (mp) REVERT: B 178 VAL cc_start: 0.8972 (t) cc_final: 0.8769 (p) REVERT: B 231 ASP cc_start: 0.9030 (t70) cc_final: 0.8378 (t0) REVERT: B 350 ASP cc_start: 0.8446 (t0) cc_final: 0.7932 (t0) outliers start: 20 outliers final: 12 residues processed: 83 average time/residue: 0.4420 time to fit residues: 39.2311 Evaluate side-chains 82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.0470 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.087748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.064793 restraints weight = 12923.454| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.95 r_work: 0.2775 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6545 Z= 0.123 Angle : 0.548 11.814 8883 Z= 0.281 Chirality : 0.039 0.128 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.128 43.654 932 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.45 % Allowed : 17.13 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.30), residues: 854 helix: 2.36 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.93 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.017 0.001 TYR A 31 PHE 0.017 0.001 PHE A 226 TRP 0.048 0.002 TRP A 239 HIS 0.001 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 6545) covalent geometry : angle 0.54770 ( 8883) hydrogen bonds : bond 0.04206 ( 518) hydrogen bonds : angle 4.11474 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.8662 (mmt) cc_final: 0.8433 (mmp) REVERT: A 350 ASP cc_start: 0.8072 (p0) cc_final: 0.7705 (p0) REVERT: A 417 MET cc_start: 0.8952 (tpt) cc_final: 0.8563 (mmm) REVERT: B 50 ASP cc_start: 0.8163 (p0) cc_final: 0.7960 (p0) REVERT: B 103 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8617 (mt-10) REVERT: B 141 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8449 (mp) REVERT: B 178 VAL cc_start: 0.8983 (t) cc_final: 0.8757 (p) REVERT: B 231 ASP cc_start: 0.9034 (t70) cc_final: 0.8391 (t0) REVERT: B 304 MET cc_start: 0.8756 (ttt) cc_final: 0.8476 (ttm) REVERT: B 350 ASP cc_start: 0.8449 (t0) cc_final: 0.7931 (t0) outliers start: 16 outliers final: 12 residues processed: 81 average time/residue: 0.4386 time to fit residues: 38.0664 Evaluate side-chains 82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.065158 restraints weight = 12762.402| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.92 r_work: 0.2770 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6545 Z= 0.124 Angle : 0.571 12.629 8883 Z= 0.287 Chirality : 0.039 0.130 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.037 42.786 932 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.45 % Allowed : 17.58 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.30), residues: 854 helix: 2.35 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.84 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 71 TYR 0.016 0.001 TYR A 31 PHE 0.018 0.001 PHE A 226 TRP 0.045 0.002 TRP A 239 HIS 0.001 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 6545) covalent geometry : angle 0.57081 ( 8883) hydrogen bonds : bond 0.04158 ( 518) hydrogen bonds : angle 4.09146 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 350 ASP cc_start: 0.8032 (p0) cc_final: 0.7685 (p0) REVERT: A 417 MET cc_start: 0.8970 (tpt) cc_final: 0.8573 (mmm) REVERT: B 50 ASP cc_start: 0.8151 (p0) cc_final: 0.7939 (p0) REVERT: B 76 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8424 (p0) REVERT: B 103 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8616 (mt-10) REVERT: B 141 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8466 (mp) REVERT: B 178 VAL cc_start: 0.8982 (t) cc_final: 0.8777 (p) REVERT: B 231 ASP cc_start: 0.9038 (t70) cc_final: 0.8373 (t0) REVERT: B 304 MET cc_start: 0.8743 (ttt) cc_final: 0.8471 (ttm) REVERT: B 350 ASP cc_start: 0.8487 (t0) cc_final: 0.7978 (t0) outliers start: 16 outliers final: 11 residues processed: 82 average time/residue: 0.4460 time to fit residues: 39.1136 Evaluate side-chains 82 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 156 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 417 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.087895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.064828 restraints weight = 12834.818| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.94 r_work: 0.2788 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6545 Z= 0.127 Angle : 0.565 12.076 8883 Z= 0.285 Chirality : 0.039 0.136 1080 Planarity : 0.003 0.035 1085 Dihedral : 5.013 43.197 932 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.29 % Allowed : 18.65 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.30), residues: 854 helix: 2.39 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.80 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 172 TYR 0.016 0.001 TYR A 31 PHE 0.016 0.001 PHE A 226 TRP 0.042 0.002 TRP A 239 HIS 0.001 0.000 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6545) covalent geometry : angle 0.56489 ( 8883) hydrogen bonds : bond 0.04176 ( 518) hydrogen bonds : angle 4.06058 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.69 seconds wall clock time: 34 minutes 22.19 seconds (2062.19 seconds total)